| Total Reads | % Aligned |
---|---|---|
rep1 | 36883730 | 97.51 |
  | Unpaired Reads | Paired Reads | Unmapped Reads | Unpaired Dupes | Paired Dupes | Paired Opt. Dupes | % Dupes |
---|---|---|---|---|---|---|---|
rep1 | 0 | 28180518 | 0 | 0 | 8590213 | 6230112 | 0.304828 |
  | Reads (QC-passed) | Reads (QC-failed) | Dupes (QC-passed) | Dupes (QC-failed) | Mapped Reads | % Mapped |
---|---|---|---|---|---|---|
rep1 | 39180610 | 0 | 0 | 0 | 39180610 | 100.00 |
  | Total Read Pairs | Distinct Read Pairs | One Read Pair | Two Read Pairs | NRF = Distinct/Total | PBC1 = OnePair/Distinct | PBC2 = OnePair/TwoPair |
---|---|---|---|---|---|---|---|
rep1 | 18904600 | 18224623 | 17609861 | 591597 | 0.964031 | 0.966268 | 29.766650 |
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
  | numReads | estFragLen | corr_estFragLen | PhantomPeak | corr_phantomPeak | argmin_corr | min_corr | phantomPeakCoef | relPhantomPeakCoef | QualityTag |
---|---|---|---|---|---|---|---|---|---|---|
rep1 | 18224623 | 0 | 0.226275795266129 | 55 | 0.2330229 | 1500 | 0.1836925 | 1.231818 | 0.863227 | 0 |
Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value
Important columns highlighted, but all/whole file can be stored for display